The Flash's Harrison Wells, played by Tom Cavanagh, is the best ambiguous villain I've encountered since Supernatural and the primary reason Season 1 of The Flash is so good (I haven't seen Season 2 yet).
What makes Harrison Wells, the character, such a good ambiguous villain is that his ambiguity is built into his motivations. Unlike many such villains, his ambiguity isn't the result of being pulled in two different directions (Crowley rather hilariously wants to be a respected king of hell, hang out with Dean Winchester, AND impress his nutty mother, somewhat incompatible goals).
Harrison Wells' desire to protect Barry Allen pulls him in the same direction as his villainy. He needs to preserve Barry's life for a certain period of time; that goal entails keeping Barry safe; keeping Barry safe involves getting to know Barry which entails a certain degree of affection.
|Impressive Jesse L. Martin as|
|remarkable Joe West|
I understand that Cavanagh reappears in Season 2. I am very pleased. Usually, I'm a fan of paying off problems within a single season, but I spent most of Season 1 thinking, "Oh, man, I hope the writers don't get rid of Wells in the end." Well, they do reveal his villainy, which disappointed me. But at least he isn't gone for good.
I have to give a shout out to two totally fun, over-the-top, non-ambiguous Flash villains: Wentworth Miller and Dominic Purcell pairing up again together as Captain Cold and Heat Wave. What a hoot!